RetrogeneDB ID: retro_pvam_967

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_19726:4099..4732(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PRPF38A
• Ensembl ID: ENSPVAG00000009803
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing A [Source:HGNC Symbol;Acc:25930]

Sequence

>retro_pvam_967
GTATGCATGTTGGGAGCATTTTACATGGAGCTGACAAACACTACAATTGATTGCTACAAGTACTTGGAGCCTCTTTGCAA
TGACTATCGAAAGATCAGGAACCAGAACTGAAACGGGGAGTTGCAACTAATGCATGTAGATGAGTTTATTGATGAACTAC
TGCACAGTGAGAGAGGCTGTGGTATCATTCTGCCCCAGCTAAAGAAATGCTATGTGATAAAGGAAGTTGAGCAACTGGAG
CCTTGGGTTAGTGCTCTAGAAGAGGACATGAATGATGTGCAGTCCAGCAAAGAGGAGGAAGGGGAGGATTAGAAGATGGA
GAGAGTACCATCGTCTGATCACTGCTGGAGAAGCTACTGAGACTTGGAGAAGCCCTGTTGCTCTCCCACACCGCACTACA
GGAAGAGTGAGAAAGGGTCTCCCAGAAGGCGGAGTCAGTCTCCCAAAAGCAGAAGTCTTTCCCCTCACCAAGGAAAGCAT
CAGAGCAAGAGTCCAAGATGTCACCACAGCAGGTCCTGAGATAGACAGCACAGATCCCACTCTAAGTCCCCAGGTCATTA
CCAAAGTCACAGACATAGGAGCCATTCAAAGTGATCTAAGAAAAACCACAGGAAGAGCTGGAGAGGGAGTGAG

Alignment

ORF - retro_pvam_967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.49 %
• Parental protein coverage: 68.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRMLGALYMRLTGTAIDCYKYLEPLYNDYRKIKSQNRNGEFELMHVDEFIDELLHSERVCDIILPRLQKR
          V.MLGA.YM.LT.T.IDCYKYLEPL.NDYRKI..QN.NGE..LMHVDEFIDELLHSER.C.IILP.L.K.
Retrocopy VCMLGAFYMELTNTTIDCYKYLEPLCNDYRKIRNQN*NGELQLMHVDEFIDELLHSERGCGIILPQLKKC

Parental  YVLEEAEQLEPRVSALEEDMDDVESSEEEEEEDEKLERVPSPDHRRRSYRDLDKPRRSPTLRYRRSRSRS
          YV..E.EQLEP.VSALEEDM.DV.SS.EEE.ED.K.ERVPS.DH..RSY.DL.KP..SPT..YR.S....
Retrocopy YVIKEVEQLEPWVSALEEDMNDVQSSKEEEGED*KMERVPSSDHCWRSY*DLEKPCCSPTPHYRKSEKXX

Parental  PRRRSRSPKRRSPSPRRERHRSKSPRRHRSRSRDRRHRSRSKSPGHHRSHRHRSHSKSPERSKKSHKKSR
          .............SP....H.SKSPR.H.SRS.DR.HRS.SKSPGH..SHRHRSHSK........H.KS.
Retrocopy XXXXXXXXXXXXXSPHQGKHQSKSPRCHHSRS*DRQHRSHSKSPGHYQSHRHRSHSK*SKK---NHRKSW

Parental  RGNE
          RG.E
Retrocopy RGSE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_967 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021594	1 retrocopy	retro_cjac_2862,
Dasypus novemcinctus	ENSDNOG00000013904	1 retrocopy	retro_dnov_443,
Homo sapiens	ENSG00000134748	2 retrocopies	retro_hsap_541, retro_hsap_545,
Gorilla gorilla	ENSGGOG00000003940	4 retrocopies	retro_ggor_493, retro_ggor_494, retro_ggor_496, retro_ggor_563,
Loxodonta africana	ENSLAFG00000025862	1 retrocopy	retro_lafr_794,
Myotis lucifugus	ENSMLUG00000001053	8 retrocopies	retro_mluc_1105, retro_mluc_1208, retro_mluc_1856, retro_mluc_2016, retro_mluc_2150, retro_mluc_2405, retro_mluc_2576, retro_mluc_828,
Monodelphis domestica	ENSMODG00000000644	1 retrocopy	retro_mdom_184,
Mus musculus	ENSMUSG00000063800	2 retrocopies	retro_mmus_1227, retro_mmus_671,
Nomascus leucogenys	ENSNLEG00000017999	2 retrocopies	retro_nleu_715, retro_nleu_719,
Oryctolagus cuniculus	ENSOCUG00000000963	1 retrocopy	retro_ocun_713,
Otolemur garnettii	ENSOGAG00000005423	1 retrocopy	retro_ogar_3216,
Petromyzon marinus	ENSPMAG00000005561	1 retrocopy	retro_pmar_28,
Pongo abelii	ENSPPYG00000001348	2 retrocopies	retro_pabe_500, retro_pabe_503,
Pan troglodytes	ENSPTRG00000000739	2 retrocopies	retro_ptro_406, retro_ptro_410,
Pteropus vampyrus	ENSPVAG00000009803	1 retrocopy	retro_pvam_967 ,
Sus scrofa	ENSSSCG00000003858	1 retrocopy	retro_sscr_924,
Ictidomys tridecemlineatus	ENSSTOG00000015610	1 retrocopy	retro_itri_1564,
Taeniopygia guttata	ENSTGUG00000008995	3 retrocopies	retro_tgut_12, retro_tgut_13, retro_tgut_14,